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Recording application executions enriched with domain semantics of computations and data Master of Science Thesis Michał Pelczar Krakow, 30.9.2008 Outline • • • • • • • • • Background Objectives Provenance model Information building Feasibility study QUaTRO State of the art Research outline Publications Background • E-Science – Advanced computing technologies supporting scientists – Global collaboration in key areas of science • Semantic Web provides data scalability – XML, RDF, RDFS, OWL – Ontology serves as taxonomy • Grid computing provides computation scalability • Virtual experiments influence scientific discoveries pace Provenance • metadata that pertains to the derivation history of a data product starting from its original sources • the seven W’s: Who, What, Where, Why, When, Which, hoW • Scientific results reproducibility • Guarantee of data reliability and quality • Regulatory mechanism of sensitive data protection • Mean of efficiency optimization ViroLab • Virtual laboratory for infectious diseases • Prevention, diagnosis and treatment • Medical science, computer science, healthcare Objectives • Design information model for provenance • Design data model for monitoring system • Adapt existing monitoring infrastructure to the provenance requirements • Define ontology creation process – – – – Ontology and data model independent Manageable Augmentable Described semantically • Design and implement component realizing the process • Incorporate the component into system grid infrastructure • Design and implement provenance querying component Provenance model • • • • • • Experiment re-execution Data dependencies Results management Performance Resources availability Related with ontologies: – Data – Domain Ontology extension • Derivation concepts – XML – Delegates • Aggregation rules • Annotations – Classes – Properties Information building • • • • • OWL and XSD independent Manageable Events correlation Events aggregation Experiment transaction support • Knowledge history tracking • Association strategy Proof of concept: Drug resistance case study • • • • Alignment Subtyping Drug ranking Different levels of semantics – Data – Computation QUaTRO • Abstract query language – Data representation and storage transparent – Understandable by non-IT specialist – Configurable by ontologies – Easy to integrate with GUI – Extendible Query processing • • • • • Provenance ontologies Mapping ontologies File systems Databases Operators Matthew Brown //*[local-name() eq 'NewDrugRanking' and ( (child::*[ name() = 'executedBy' and . eq 'MrHyde']))] executedBy NewDrugRanki ng dateOfBloodSample 2007-06-28 //*[local-name() eq 'NewDrugRanking' and ( (child::*[ name() = 'dateOfBloodSample' and . eq '200706-28']))] usedRuleSet //*[local-name() eq 'NewDrugRanking' and (child::*[ name() = 'usedRuleSet' and (@*[name()='rdf:resource' and ( ( . eq 'http://www.virolab.org/onto/ drs-protos/HIVDB_4_2_7' )) ]) ])] HIVDB SELECT id FROM rulesets WHERE name = ‘HIVDB’ 4.2.8 SELECT id FROM rulesets WHERE version = ‘4.2.8’ name RulSet version //*[local-name() eq 'RuleSet' and ( (child::*[ name() = 'vl-dataprotos:dasId' and . eq 'cyfronet_mysql:test:id:2']))] Summary • Data model for operations and resources • Ontologies for data, experiments and geno2drs scenario • Monitoring infrastructure: remote logging, automatic generation of helpers • Semantic Event Aggregator implemented and deployed as OneJAR application • QUaTRO integrated into GridSphere portal Future work • QUaTRO extensions – Join operation – Provenance graph rendering – File system querying • Model extensions – Performance recording – Data origin recording • Explicit provenance recording – Domain ontologies generation – Partial results storage – Domain events publication Publications • B. Balis, M. Bubak, M. Pelczar, From Monitoring Data to Experiment Information – Monitoring of Grid Scientific Workflows. In G. Fox, K. Chiu, and R. Buyya, editors, Third IEEE International Conference on e-Science and Grid Computing, e-Science 2007, Bangalore, India, 10-13 December 2007, pages 187-194. IEEE Computer Society, 2007. • B. Balis, M. Bubak, M. Pelczar, J. Wach, Provenance Tracking and Querying in ViroLab. In Cracow GridWorkshop 2007Workshop Proceedings, pp.71-76, ACC CYFRONET AGH 2008. • B. Balis, M. Bubak, M. Pelczar, J. Wach, Provenance Querying for End-Users: A Drug Resistance Case Study. In: Bubak, M., Albada, G.D.v., Dongarra, J., Sloot, P.M.A. (Eds.), Proceedings ICCS 2008, Krakoland, June 23-25, 2008, LNCS 5103, pp. 80-89, Springer 2008. Detailed information • ViroLab: http://www.virolab.org • VLvl: http://www.virolab.cyfronet.pl http://grid.cyfronet.pl/virolab/wiki • QUaTRO: http://virolab.cyfronet.pl/trac/quatro • Ontologies: http://virolab.cyfronet.pl/onto